Variant report

Variant	rs2838448
Chromosome Location	chr21:45373304-45373305
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr21:45372743-45373309	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:45370723..45373935-chr21:45374637..45377762,3	K562	blood:
2	chr1:150253102..150255940-chr21:45372108..45374066,2	MCF-7	breast:
3	chr21:45371946..45375677-chr21:45376772..45380405,4	K562	blood:
4	chr21:45371704..45374337-chr21:45426756..45428493,2	K562	blood:
5	chr21:45368958..45371465-chr21:45372849..45375980,3	K562	blood:
6	chr21:45365116..45368184-chr21:45371047..45373438,4	K562	blood:
7	chr21:45371594..45373421-chr21:45394016..45396478,2	K562	blood:
8	chr21:45365752..45369442-chr21:45370702..45375252,7	MCF-7	breast:

No data

Variant related genes	Relation type
AGPAT3	TF binding region
ENSG00000160216	Chromatin interaction
ENSG00000159208	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11910604	0.85[CHB][hapmap]
rs2000787	0.85[JPT][hapmap]
rs2003774	0.86[CHB][hapmap]
rs2329630	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2838452	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs2838459	1.00[CHB][hapmap]
rs2838463	1.00[CHB][hapmap];0.86[GIH][hapmap]
rs3737358	0.86[CHB][hapmap]
rs3737360	0.81[ASN][1000 genomes]
rs3788089	0.81[LWK][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes]
rs59464702	1.00[EUR][1000 genomes]
rs6518340	0.85[JPT][hapmap]
rs73371158	1.00[EUR][1000 genomes]
rs73371178	1.00[EUR][1000 genomes]
rs73371191	1.00[EUR][1000 genomes]
rs73373123	1.00[EUR][1000 genomes]
rs73906640	1.00[EUR][1000 genomes]
rs878132	0.85[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531545	chr21:45095397-45395904	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	esv33817	chr21:45169412-46031810	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
3	nsv913887	chr21:45344799-45670770	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	nsv913888	chr21:45351206-45428278	Genic enhancers Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv1055772	chr21:45353436-45373304	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv913889	chr21:45361044-45414119	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2838448	AGPAT3	cis	lymphoblastoid	seeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45343800-45379800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr21:45359200-45376000	Weak transcription	HUVEC	blood vessel
3	chr21:45359200-45378800	Weak transcription	NHEK	skin
4	chr21:45359200-45379000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr21:45359400-45376000	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr21:45359400-45389000	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr21:45359800-45376400	Weak transcription	NHLF	lung
8	chr21:45361000-45379200	Weak transcription	Ovary	ovary
9	chr21:45363600-45377000	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr21:45364800-45378400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr21:45367200-45376600	Weak transcription	Pancreas	Pancrea
12	chr21:45367200-45379200	Weak transcription	Fetal Brain Female	brain
13	chr21:45368400-45379400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr21:45368400-45379800	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr21:45368600-45374000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr21:45368600-45374600	Weak transcription	Gastric	stomach
17	chr21:45369000-45376400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr21:45369200-45379400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr21:45369400-45375800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr21:45369400-45378200	Weak transcription	K562	blood
21	chr21:45369400-45378600	Weak transcription	HepG2	liver
22	chr21:45369400-45379800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr21:45369400-45388800	Weak transcription	Colon Smooth Muscle	Colon
24	chr21:45369600-45374400	Weak transcription	Esophagus	oesophagus
25	chr21:45369600-45376000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr21:45369600-45376000	Strong transcription	Fetal Stomach	stomach
27	chr21:45369600-45376200	Weak transcription	Brain Hippocampus Middle	brain
28	chr21:45369600-45376200	Weak transcription	Fetal Lung	lung
29	chr21:45369600-45376400	Weak transcription	Adipose Nuclei	Adipose
30	chr21:45369600-45376400	Weak transcription	Brain Anterior Caudate	brain
31	chr21:45369600-45376400	Weak transcription	Brain Substantia Nigra	brain
32	chr21:45369600-45376400	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr21:45369600-45378200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr21:45369600-45379000	Weak transcription	Brain Angular Gyrus	brain
35	chr21:45369600-45379200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr21:45369600-45379400	Weak transcription	Aorta	Aorta
37	chr21:45369600-45381200	Weak transcription	Primary hematopoietic stem cells	blood
38	chr21:45369800-45378200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr21:45369800-45379400	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr21:45370000-45376400	Weak transcription	Primary B cells from peripheral blood	blood
41	chr21:45370000-45377200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr21:45370000-45377400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr21:45370000-45378200	Weak transcription	Dnd41	blood
44	chr21:45370000-45378600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr21:45370000-45379200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr21:45370000-45379600	Weak transcription	Brain Germinal Matrix	brain
47	chr21:45370000-45381200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr21:45370000-45384000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr21:45370000-45390200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr21:45370200-45378600	Weak transcription	Thymus	Thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links